5-154830815-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032385.5(FAXDC2):c.352G>A(p.Gly118Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000186 in 1,613,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032385.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAXDC2 | NM_032385.5 | c.352G>A | p.Gly118Ser | missense_variant | Exon 5 of 9 | ENST00000326080.10 | NP_115761.2 | |
FAXDC2 | XM_006714753.3 | c.352G>A | p.Gly118Ser | missense_variant | Exon 6 of 10 | XP_006714816.1 | ||
FAXDC2 | XM_047416652.1 | c.-69G>A | 5_prime_UTR_variant | Exon 2 of 6 | XP_047272608.1 | |||
FAXDC2 | XM_047416654.1 | c.-55+3810G>A | intron_variant | Intron 1 of 4 | XP_047272610.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000481 AC: 12AN: 249568Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135394
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461776Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727198
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.352G>A (p.G118S) alteration is located in exon 5 (coding exon 4) of the FAXDC2 gene. This alteration results from a G to A substitution at nucleotide position 352, causing the glycine (G) at amino acid position 118 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at